The Shastry-Sutherland model and its generalizations have been shown to capture emergent complex magnetic properties from geometric frustration in several quasi-two-dimensional quantum magnets. Using an sd exchange model, we show here that metallic Shastry-Sutherland magnets can exhibit a topological Hall effect driven by magnetic skyrmions under realistic conditions. The magnetic properties are modeled with competing symmetric Heisenberg and asymmetric Dzyaloshinskii-Moriya exchange interactions, while a coupling between the spins of the itinerant electrons and the localized moments describes the magnetotransport behavior. Our results, employing complementary Monte Carlo simulations and a novel machine learning analysis to investigate the magnetic phases, provide evidence for field-driven skyrmion crystal formation for an extended range of Hamiltonian parameters. By constructing an effective tight-binding model of conduction electrons coupled to the skyrmion lattice, we clearly demonstrate the appearance of the topological Hall effect. We further elaborate on the effects of finite temperatures on both magnetic and magnetotransport properties.